Identification and Validation of Protein Biomarkers for Invasive Aspergillosis; Development of Surface-Induced Dissociation Device and Paper Spray Ionization Source for Protein Complex Studies

Abstract

The research described in this dissertation is divided into two sections. The first section focuses on mass spectrometry-based bottom-up proteomics application to identify fungal protein biomarkers of invasive aspergillosis infection. The second part focuses on instrument development to improve current ionization and dissociation technologies for characterizing topology and substructure of protein complexes. Part I of this dissertation describes the identification and validation of protein biomarkers for Invasive Aspergillosis (IA), a fatal pulmonary infection. Aspergillus fumigatus, the organism responsible for this disease, is an opportunistic fungus. Immunocompromised individuals can suffer from IA due to impaired immune response. The current diagnostic tools are time-consuming and have variable sensitivity and specificity. Hence, treatments for IA are often administered too late. The goal of this research is to use mass spectrometry to identify and validate novel fungal protein biomarkers for IA. To tackle this challenge, several systems were studied. Commercial Aspergillus antigen was used for method development, and to serve as standards for spiking and comparison. Mouse models of different disease manifestations were used in the initial study to compare proteomic differences in carefully controlled disease states. Although it was not successful in providing candidate biomarkers, the mouse samples provided host response protein data. Human patient samples yielded the most promising results. Several Aspergillus proteins have been identified and validated from patient bronchoalveolar lavage fluid, and could have the potential to be later used on a diagnostic platform. Part II describes two instrument development projects: incorporation of a surface-induced dissociation device into a commercial ion mobility time-of-flight mass spectrometer, and the development of a paper spray ionization source. Protein complexes are often studied using collision-induced dissociation (CID), which does not provide enough substructure information. Surface-induced dissociation (SID) allows access to higher energy fragmentation pathways, which generates more useful substructure information. Its potential is demonstrated with three systems here-- one metal cluster and two protein complexes. All systems show that SID can provide more useful structural information than CID under similar conditions. The development of a paper spray (PS) source for protein complex ionization provides another way to study protein complexes. Chapter 9 shows that this ionization method can also be applied to protein complexes. Under the same conditions as its nanospray counterpart, similar mass spectra can be obtained using PS. This exciting result is the first demonstrations that PS can be used for protein complexes while maintaining each protein complex's native structure and conformation.